DNA Replication Process

DNA Polymerase

• Enzyme for building new DNA strands
• Adds free nucleotides to existing DNA strands
• Follows base-pairing rules (A with T, C with G)

DNA Replication

• Semi-conservative process
• Each new DNA molecule has one original strand and one new strand

Process of DNA replication

• DNA Polymerase: Builds new DNA strands, adding nucleotides following base-pairing rules
• Helicase: Unwinds and separates the original DNA double helix, creating a replication fork
• Leading Strand: Synthesized continuously in the 5' to 3' direction as DNA unwinds
• Lagging Strand: Synthesized discontinuously in short Okazaki fragments due to opposite direction
• Original DNA: Template for synthesizing new DNA strands, each strand serving as template for a new complementary strand

Initial State of DNA replication

• Double-stranded DNA molecule needs replication
• Eukaryotes have multiple origins of replication to speed up the process

Replication Bubble Formation

• Helicase unwinds the double helix at the origin of replication which separates strands creating the replication bubble

Replication Fork

• Y-shaped structures within the replication bubble where DNA is actively unwound
• Proceeds in both directions away from the origin

DNA Polymerase and Strand Synthesis

• DNA polymerase adds new nucleotides to separated strands to build complementary strands
• Synthesis is not simultaneous for both strands

Leading and Lagging Strands

• Leading strand is synthesized continuously in the 5' to 3' direction
• Lagging strand is synthesized discontinuously in Okazaki fragments because DNA polymerase can only build in the 5' to 3' direction
• Polymerase must work against the replication fork direction for the lagging strand

Completion of DNA replication

• Two identical DNA molecules are created, each with one original and one new strand through a semi-conservative replication
• Each new molecule is completely double-stranded

Original (Parent DNA)

• Double-stranded DNA molecule being replicated
• The double helix unwinds at a specific point

Helicase

• Enzyme unwinds the DNA double helix at the replication fork, separating parental strands

Primase

• Synthesizes short RNA primers crucial for starting DNA synthesis, providing a 3'-OH group for DNA polymerase to add nucleotides to
• RNA primers are in place on both the leading and lagging strands

DNA Polymerase

• Adds nucleotides to the 3' end of the growing DNA strand, following base-pairing rules (A with T, and C with G) and works on both the leading and lagging strands

Leading Strand

• DNA synthesis occurs continuously in the 5' to 3' direction
• Only one primer is needed

Lagging Strand

• DNA synthesis is discontinuous, creating Okazaki fragments
• Multiple RNA primers are needed and each Okazaki fragment requires a new primer

Okazaki Fragments

• Short, newly synthesized DNA fragments on the lagging strand

Topoisomerase

• Relieves the torsional strain caused by unwinding the DNA ahead of the replication fork to prevent supercoiling and is not directly involved in synthesis

RNA Primers

• Short RNA sequences provide a starting point for DNA polymerase
• These are later removed and replaced with DNA

Contrast Between Leading and Lagging Strand Synthesis During DNA Replication

Top (Leading Strand)

• Leading strand is synthesized continuously in the 5' to 3' direction, allowing DNA polymerase to add nucleotides to the 3' end without interruption

Bottom (Lagging Strand)

• Lagging strand is synthesized discontinuously because DNA polymerase can only synthesize in the 5' to 3' direction
• Lagging strand must be synthesized in short fragments as the replication fork progresses

Okazaki Fragments

• Short DNA fragments synthesized on the lagging strand and each requires a separate RNA primer indicated by small circles

RNA Primers

• Short RNA sequences that provide a starting point for DNA polymerase

Ligase

• Enzyme joins Okazaki fragments to form a continuous strand indicated by the label connecting the Okazaki fragments

5' End Replication

• Synthesis of Okazaki fragments happens in a way that the new DNA is added to the 5' end of the previous Okazaki fragment

Primer-placed nucleotides

• Newly added nucleotides to the 5' end of each Okazaki fragment

Simplified Representation of Replication Fork

• Focuses on the difference between leading and lagging strand synthesis

Parental DNA

• Original double-stranded DNA molecule at top with the 5' and 3' ends of each strand indicated

Replication Fork

• Y-shaped structure where the DNA strands are separating

Leading Strand

• Synthesized continuously in the 5' to 3' direction and the arrow indicates the direction of synthesis

Lagging Strand

• Synthesized discontinuously in Okazaki fragments with arrows indicating the direction of synthesis, opposite to the movement of the replication fork

Okazaki Fragments

• Short DNA fragments that make up the lagging strand are highlighted

3 Models of DNA replication

• Conservative: The original parental DNA remains intact, and a completely new DNA molecule is synthesized
• Semi-conservative: Each new DNA molecule has one original strand and one newly synthesized strand (correct model)
• Dispersive: Parental DNA is dispersed throughout both new DNA molecules

Transcription

• Is the first step in gene expression
• Information encoded in a DNA sequence is copied into a messenger RNA (mRNA) molecule

DNA (Deoxyribonucleic Acid)

• Original genetic material
• Contains a segment of DNA with a sequence of bases, 3'-ATGAGTCCAAGT-5'
• Complementary strand is 5'-TACTCAGGTTCA-3'
• Adenine (A) pairs with Thymine (T), and Guanine (G) pairs with Cytosine (C)

Transcription

• DNA sequence is used as a template to create an mRNA molecule
• Enzyme RNA polymerase is responsible

mRNA (Messenger Ribonucleic Acid)

• RNA copy of the DNA sequence
• mRNA sequence produced from the DNA template: 5'-UACUCAGGUUCA-3'
• Uracil (U) replaces Thymine (T), so A pairs with U

Codons

• Three-nucleotide sequences in mRNA that specify amino acids during protein synthesis translation
• mRNA sequence is divided into codons

Stages of Transcription

• Initiation: RNA polymerase binds to the promoter (DNA region) and DNA unwinds allowing polymerase access to the template strand
• Elongation: RNA polymerase moves along the template strand to synthesizing a complementary RNA molecule in the 5' to 3' direction obeying base-pairing rules
• Termination: Transcription ends when RNA polymerase reaches termination sequence
• Polymerase detaches, releasing the RNA molecule, DNA rewinds

Processing of pre-mRNA into mature mRNA in eukaryotes

• Transcription begins with RNA polymerase II, using DNA template to synthesize a pre-mRNA molecule
• Pre-mRNA has a promoter (DNA region that signals start of transcription), exons (coding sequences), introns (non-coding sequences interspersed between exons), 5' UTR and 3' UTR (untranslated regions playing roles in translation)

5' Capping and 3' Poly(A) Tail Addition

• 5' GTP cap is added to the 5' end protect mRNA, and helps ribosome binding
• Poly(A) tail (string of adenine nucleotides) is added to the 3' end and protects/aids in export from the nucleus

RNA Splicing

• Introns removed, exons joined to form continuous protein-coding sequence by a spliceosome

Mature mRNA

• mRNA contains exons, 5' cap and 3' poly(A) tail and is ready for translation

Translation

• Mature mRNA is transported to ribosomes where protein-coding sequence becomes a polypeptide chain protein

Transcription and Translation

• Fundamental steps in gene expression in a cell

Transcription

• Occurs in cell nucleus and involves RNA polymerase unwinding a segment of DNA
• Enzyme uses one DNA strand as template to synthesize of messenger RNA (mRNA)
• mRNA transported out of the nucleus into the cytoplasm

Translation

• Takes place in the cell cytoplasm and binds to ribosomes
• Ribosome moves along mRNA reading it in nucleotides called codons
• Transfer RNA (tRNA) with amino acids, recognizes and binds to the codons on mRNA
• Ribosome links amino acids together forming polypeptide chain
• This continues till a stop codon is reached
• Polypeptide chain is released from ribosome, and folds into a protein

Types of RNA involved in protein synthesis

• mRNA: carries genetic code as a single-stranded molecule
• tRNA: acts as an adapter molecule between mRNA and amino acids
• rRNA: forms the structural and catalytic core of the ribosome

Codon table

• Translates mRNA into an amino acid sequence (codon) and is used to find the first, second and third base of codon
• The codon AUG codes for Methionine (Met), also acts as a start codon
• UAA, UAG, and UGA are stop codons for protein synthesis

Gametogenesis

• Biological process of producing gametes (sex cells)

2 types of gametogenesis

• Oogenesis (female gametes production): A diploid (2n) primary oocyte undergoes meiosis I to produce a haploid (n) secondary oocyte and a polar body. A secondary oocyte undergoes meiosis II resulting in a haploid ovum
• Spermatogenesis (male gametes production): A diploid (2n) primary spermatocyte undergoes meiosis I to produce two haploid (n) secondary spermatocytes.

Fertilization

• Fusion of haploid ovum and sperm
• Restores the diploid (2n) chromosome number resulting in the zygote

Sexual reproduction

• Fusion of sperm and egg (gametes) to form a zygote
• Zygote has genetic material from both parents and is the first developmental stage of a new organism

Meiosis

• Illustration of how the process of gametogenesis contributes to genetic diversity
• Meiosis 1 is a cell division that reduces chromosome number by half (haploid)
• Two equal arrangements of homologous chromosomes at Metaphase lead to different combinations
• Independent assortment of chromosomes in meiosis and crossing over during combination of genes

Spermatogenesis

• The production of sperm in the testes and takes in the seminiferous tubules

Key stages of spermatogenesis

• Spermatogonium: diploid stem cells on the basement membrane which undergoes mitosis to produce primary spermatocytes, which are still diploid
• Meiosis I: primary spermatocyte undergoes meiosis (reductional division), producing two haploid secondary spermatocytes which Meiosis II (equational division), making two haploid round spermatids
• Round Spermatids undergo spermiogenesis, which is a process of differentiation, making mature (spermatozoa sperm)

Spermiogenesis

• Final stage where spermatids develop to mature spermatozoa
• Golgi Apparatus Activity: packages enzymes into the acrosomal vesicle.
• Acrosome formation: Acrosomal vesicle forms a cap-like structure with enzymes for fertilization
• Nuclear Condensation: Nucleus becomes condensed reducing volume and increasing density

Flagellum Development

• Flagellum develops for sperm motility and mitochondria aggregate in providing energy

Hormonal Control of Spermatogenesis

• Hypothalamus: Releases GnRH
• Anterior pituitary: Stimulates pituitary to release FSH and LH
• Testes: FSH acts on Sertoli cells in seminiferous tubules to support spermatogenesis and produce ABP (androgen-binding protein). LH acts on Leydig cells, stimulating testosterone production.

Oogenesis

• Formation of eggs in the ovaries and divided into Follicular, Ovulation and Luteal phases

Key stages of oogenesis

• Primary Oocyte (2n): Diploid cell, that begins meiosis I generating one mature ovum per cycle
• Meiosis 1: The primary oocyte undergoes meiosis, producing a secondary oocyte (n) and a first polar body (n)
• Secondary Oocyte (ii): Secondary oocyte proceeds to meiosis II only if fertilization
• Meiosis II: Secondary oocyte completes meiosis after fertilization producing a mature ovum (n) and a second polar body (n) Ovum (n): mature haploid egg cell

Hormonal Control of Oogenesis

• Hypothalamus: Releases GnRH
• Pituitary: GnRH stimulates the pituitary to release LH and FSH
• Ovary: LH and FSH stimulate ovaries to produce estrogen and progesterone, effect on uterine lining with feedback to hypothalamus and pituitary
• Uterus: Estrogen and progesterone prepare for potential implantation

Fertilization

• Fusion of haploid ovum with a sperm to make a diploid zygote containing genetic material. Only one ovum produced, where spermatogenesis makes four sperm

Significance of gametogenesis

• Process of crossing over during meiosis between homologous chromosomes to result in recombination of DNA segements

Sperm Defects

• Head Defects: Abnormal head shapes of sperm
• Midpiece Defects: Defects impede motility of sperm
• Tail Defects: Abnormal tails reduce sperm motility
• Acrosomeless: Lack of acrosome prevents the sperm from penetrating the egg

Normal Karyotype

• Normal human karyotype is used to compare against gamete abnormalities
• Genetic abnormalities lead to disorders in sex organs

Cyclical Parthenogenesis

• Type of reproduction with alternating generations of sexual and asexual

Gametogenesis in Plants

• The female gametophyte has specific locations and components vital for fertization

Double Fertilization

• A defining characteristic for flowering plants which results in simultaneous development of both the embryo and endosperm

Environmental Factors Affecting Gametogenesis

• BPA production and release: produced industrially and it contaminates bodies of water
• BPA biomagnification: BPA accumulate in organisms increasing/altering within said organisms
• Toxic Effects: Causes potential disruption withing the endocrine system
• Metabolic Pathway: Fungi have been shown to degrade BPA, although this has limitations still

Stem Cells

• Diagrams of both males and females are shown representing stages of gametogenesis
• Stem cell research has relevance and possibilities for infertility, modeling diseases, and developing gametogenesis etc

What is Gametogenesis?

• Early Embryonic Development: early stages of development are displayed after fertilization

Genes as Instruction Manuals

• Heredity that contains of instruction/maintain of what an organism is

Central Dogma of biology

• Transcription, mRNA, then translated into protein

In essence

• Genes (DNA) provide instruction, using transcription to creates proteins

Cell Specialization

• Is when a pluripotent cell can differentiate, leading to specialized cells

specialized cells

• Sex
• Muscle
• Fat
• Bone
• Immune
• Epithelial
• Nervous
• Blood

All cells differ as development proceeds

cell structure

• Undergo with processes, aquiring specialized structures essential, creation of tissues, organ, organism.

organization level

• Cells basic unit
• Tissue group of cells
• Organ T.o tissue working together
• Organ system group of organs wok together for complex function

pattern formation (level cellular)

• Cleavage: cell growth w out substantial increase

Main Stages

• Transcription(nucleus) DNA, one is used for synthesis
• translation in the cytoplasm-mRNA molecules moved by a ribosome

Turning genes on and off: regulation

• Genes are active. "gene expression"-used sythesize, genes used and made

Cellular Signaling

• Transmissions across neurons

Growth and Form

• Sign Transduction steps by which cells respond

main steps

• Reaction, signal, then transducer leads to response

Control gene

• As homeotic ensures layout is maintained, by building bodies

Studying How Genes Works

• 1 making random material and screen change by undering phenotype

Comparing Genetics

• Highlighted steps included gene silencing, and mutation occurs over year. But new gene has fast strain selection

Genetics: Step

• Reverse and starts known gene

CRISPR9

• Gene editing that can recognize/cleves to edit genes used for application ex; agriculture

RNA interference(silent)

RnA1 process

• dsRNA, Dicer cleaves of into srRNA

Home genes

• Role for animal devopement, are arranged/location cluster corresponding to where the genes are showing the axis with body

Body evolution related

• Tree showing genes relationships

Evolution

• Increasing of more Hox

In other words

• Bodies are complex compared to simpler versions